Target - Succinate Dehydrogenase (Flavoprotein subunit) SDHA (Succinic dehydrogenase) (Fumarate reductase) (Fumarate dehydrogena)

* (protein/gene name): SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT [Mycobacterium tuberculosis]
*NCBI Gene # or RefSeq#: 532538596
*Protein ID (NP or XP #) or Wolbachia#: Rv3318
*Organism (including strain): Mycobacterium tuberculosis
Etiologic Risk Group (see link below): 3
http://www.absa.org/riskgroups/bacteriasearch.php?genus=Mycobacterium&species=tuberculosis

*Backgound/Disease Information (sort of like the Intro to your Mini Research Up): Mycobacterium tuberculosis (MTB) is a pathogenic bacterial species in the family Mycobacteriaceae and the causative agent of most cases of tuberculosis. Robert Koch first discovered M. tuberculosis in 1882, revealing that MTB has an unusual, waxy coating on its cell surface which makes the cells impervious to Gram staining, therefore acid-fast detection techniques are used instead. The physiology of M. tuberculosis is highly aerobic and requires high levels of oxygen. MTB, primarily a pathogen of the mammalian respiratory system, infects the lungs. Today, the most frequently used diagnostic methods for TB are the tuberculin skin test, acid-fast stain, and chest radiographs.

Link to TDR Targets page (if present): http://tdrtargets.org/targets/view?gene_id=9874

Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.): http://www.ncbi.nlm.nih.gov/protein/EQM22493.1

Essentiality of this protein:
Rv3318 has essentiality data
Gene/Ortholog: mtu3378 (OG4_10363); Phenotype: non-essential; Source study: nmpdr
Gene/Ortholog: eco701 (OG4_10363); Phenotype: undefined; Source study: blattner
Gene/Ortholog: eco701 (OG4_10363); Phenotype: non-essential; Source study: gerdes
Gene/Ortholog: eco701 (OG4_10363); Phenotype: non-essential; Source study: keio
Gene/Ortholog: eco701 (OG4_10363); Phenotype: non-essential; Source study: shigen
Gene/Ortholog: eco4000 (OG4_10363); Phenotype: non-essential; Source study: blattner
Gene/Ortholog: eco4000 (OG4_10363); Phenotype: non-essential; Source study: gerdes
Gene/Ortholog: eco4000 (OG4_10363); Phenotype: non-essential; Source study: keio
Gene/Ortholog: eco4000 (OG4_10363); Phenotype: non-essential; Source study: shigen
Gene/Ortholog: cel3359 (OG4_10363); Phenotype: Embryonic Lethal/; Source study: neb
Gene/Ortholog: cel3359 (OG4_10363); Phenotype: Larval/Adult Lethal/; Source study: neb
Gene/Ortholog: cel940 (OG4_10363); Phenotype: Growth Defect; Source study: neb
Gene/Ortholog: cel940 (OG4_10363); Phenotype: Embryonic Lethal/; Source study: neb
Gene/Ortholog: cel940 (OG4_10363); Phenotype: Morphology Defect; Source study: neb
Gene/Ortholog: cel3359 (OG4_10363); Phenotype: Embryonic Lethal/Arrest; Source study: wormbase
Gene/Ortholog: cel940 (OG4_10363); Phenotype: Embryonic Lethal/Arrest; Source study: wormbase
Gene/Ortholog: Tb927.8.6580 (OG4_10363); Phenotype: significant gain of in bloodstream forms (3 days); Source study: alsford
Gene/Ortholog: Tb927.8.6580 (OG4_10363); Phenotype: significant gain of in bloodstream forms (6 days); Source study: alsford
Gene/Ortholog: Tb927.8.6580 (OG4_10363); Phenotype: no significant loss or gain of in procyclic forms; Source study: alsford
Gene/Ortholog: Tb927.8.6580 (OG4_10363); Phenotype: significant gain of fitness in differentiation of procyclic to bloodstream forms; Source study: alsford

Complex of proteins?: n/a
Druggable (list number or cite evidence from a paper/database showing druggable in another organism): 0.7

*EC#: 1.3.99.1
Link to BRENDA EC# page: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.3.99.1

Figure 1: Screenshot of of BRENDA enzyme mechanism schematic.

Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):

Anti-SDHA (131-145) antibody produced in rabbit
Catalog Number: SAB1100429
Cost: $317.50
Supplier: Sigma-Aldrich

-- link to Sigma (or other company) page for assay (see Sigma links below)
http://www.sigmaaldrich.com/catalog/product/sigma/sab1100429?lang=en®ion=US

Structure (PDB or Homology model)
PDB #: 2LFC
http://www.rcsb.org/pdb/results/results.do?qrid=EEF61829&tabtoshow=Current

Current Inhibitors:
CHEMBL1170848
CHEMBL1170849
CHEMBL1170850
CHEMBL1170851
http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pubmed.jsp?pubmed=50031969&pubmed_submit=TBD

Expression Information (has it been expressed in bacterial cells): Yes, in E. coli cells.

Image of protein:

Figure 2: Pymol representation of 2LFC protein shown as sticks and colored by element with green carbons.

*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):

<span style="background-color: #ffffff; font-family: monospace,serif;"><span class="ff_line">MSTDIPATVSAETVTSWSDDVDVTVIGFGIAGGCAAVSAAAAGARVLVLERAAAAGGTTALAGGHFYLGG
GTTVQLATGHPDSPEEMYKYLVAVSREPDHDKIRAYCDGSVEHFNWLEGLGFQFERSYFPGKAVIQPNTE
GLMFTGNEKVWPFLELAVPAPRGHKVPVPGDTGGAAMVIDLLLKRAASLGIQIRYETGATELIVDGTGKV
TGVMWKRFSETGAIKAKSVIIAAGGFVMNPDMVAKYTPKLAEKPFVLGNTYDDGLGIRLGVSAGGATQHM
DQMFITAPPYPPSILLTGIIVNKLGQRFVAEDSYHSRTAGFIMEQPDSAAYLIVDEAHLEHPKMPLVPLI
DGWETVVEMEAALGIPPGNLAATLDRYNAYAARGADPDFHKQPEFLAAQDNGPWGAFDMSLGKAMYAGFT
LGGLATSVDGQVLRDDGAVVAGLYAVGACASNIAQDGKGYASGTQLGEGSFFGRRAGAHAAARAQGM</span></span>

*length of your protein in Amino Acids: 417
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 44.3985 kDa

Ext. coefficient    49975
Abs 0.1% (=1 g/l)   1.126, assuming all pairs of Cys residues form cystines
 
 
Ext. coefficient    49850
Abs 0.1% (=1 g/l)   1.123, assuming all Cys residues are reduced</span>

http://web.expasy.org/cgi-bin/protparam/protparam
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.

Figure 3: TMpred graph image derived from website by inputting amino acid sequence.

*CDS Gene Sequence (paste as text only):
atgagcaccgatattccggcgaccgtgagcgcggaaaccgtgaccagctggagcgatgat gtggatgtgaccgtgattggctttggcattgcgggcggctgcgcggcggtgagcgcggcg gcggcgggcgcgcgcgtgctggtgctggaacgcgcggcggcggcgggcggcaccaccgcg ctggcgggcggccatttttatctgggcggcggcaccaccgtgcagctggcgaccggccat ccggatagcccggaagaaatgtataaatatctggtggcggtgagccgcgaaccggatcat gataaaattcgcgcgtattgcgatggcagcgtggaacattttaactggctggaaggcctg ggctttcagtttgaacgcagctattttccgggcaaagcggtgattcagccgaacaccgaa ggcctgatgtttaccggcaacgaaaaagtgtggccgtttctggaactggcggtgccggcg ccgcgcggccataaagtgccggtgccgggcgataccggcggcgcggcgatggtgattgat ctgctgctgaaacgcgcggcgagcctgggcattcagattcgctatgaaaccggcgcgacc gaactgattgtggatggcaccggcaaagtgaccggcgtgatgtggaaacgctttagcgaa accggcgcgattaaagcgaaaagcgtgattattgcggcgggcggctttgtgatgaacccg gatatggtggcgaaatataccccgaaactggcggaaaaaccgtttgtgctgggcaacacc tatgatgatggcctgggcattcgcctgggcgtgagcgcgggcggcgcgacccagcatatg gatcagatgtttattaccgcgccgccgtatccgccgagcattctgctgaccggcattatt gtgaacaaactgggccagcgctttgtggcggaagatagctatcatagccgcaccgcgggc tttattatggaacagccggatagcgcggcgtatctgattgtggatgaagcgcatctggaa catccgaaaatgccgctggtgccgctgattgatggctgggaaaccgtggtggaaatggaa gcggcgctgggcattccgccgggcaacctggcggcgaccctggatcgctataacgcgtat gcggcgcgcggcgcggatccggattttcataaacagccggaatttctggcggcgcaggat aacggcccgtggggcgcgtttgatatgagcctgggcaaagcgatgtatgcgggctttacc ctgggcggcctggcgaccagcgtggatggccaggtgctgcgcgatgatggcgcggtggtg gcgggcctgtatgcggtgggcgcgtgcgcgagcaacattgcgcaggatggcaaaggctat gcgagcggcacccagctgggcgaaggcagcttttttggccgccgcgcgggcgcgcatgcg gcggcgcgcgcgcagggcatg


*GC% Content for gene: Not .
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): Not .
*GC% Content for gene (codon optimized): Not Available.

Do Not Need this info for Spring (but still copy these lines to your page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.

Primer design results for 'tail' primers (this is just 2 sequences):
**